should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA

See #2611.

should-get-tests/*.should-get: replace $VIDJIL_DIR/data by $VIDJIL_DATA
See #2611.
880abf7d · Mathieu Giraud · 35525c10 · 880abf7d · 880abf7d · 880abf7d
Commit 880abf7d authored Sep 13, 2017 by Mathieu Giraud
--- a/algo/tests/should-get-tests/10-md5-data.should-get
+++ b/algo/tests/should-get-tests/10-md5-data.should-get
 !NO_LAUNCHER:
-!LAUNCH: (cd $VIDJIL_DIR/data ; md5sum *.fasta || md5 -r *.fasta)
+!LAUNCH: (cd $VIDJIL_DATA ; md5sum *.fasta || md5 -r *.fasta)

 $ Check md5 in data/
 1:985219d9156b6d9e8966807595beada3 Stanford_S22.fa

--- a/algo/tests/should-get-tests/ambiguous_representative.should-get
+++ b/algo/tests/should-get-tests/ambiguous_representative.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DIR/data/toy_V.fa -J $VIDJIL_DIR/data/toy_J.fa $VIDJIL_DIR/data/ambiguous_representative.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -r 1 -k 4 -w 20 -z 0 -c clones -V $VIDJIL_DATA/toy_V.fa -J $VIDJIL_DATA/toy_J.fa $VIDJIL_DATA/ambiguous_representative.fa

 $ Short reads properly segmented
 1:SEG_+.* -> .* 4

--- a/algo/tests/should-get-tests/ambiguous_representative2.should-get
+++ b/algo/tests/should-get-tests/ambiguous_representative2.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DIR/data/test_representatives.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -c clones -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/test_representatives.fa

 $ Three clones should be found
 1:3 clones

--- a/algo/tests/should-get-tests/cdr3-stopcodon.should-get
+++ b/algo/tests/should-get-tests/cdr3-stopcodon.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DIR/data/cdr3-stopcodon.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -3 -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG $VIDJIL_DATA/cdr3-stopcodon.fa
 !LOG: out/cdr3-stopcodon.vidjil

 $ Two identical junctions in JSON

--- a/algo/tests/should-get-tests/cgi-align.should-get
+++ b/algo/tests/should-get-tests/cgi-align.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/cgi-align2.should-get
+++ b/algo/tests/should-get-tests/cgi-align2.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa2.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa2.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/cgi-align3.should-get
+++ b/algo/tests/should-get-tests/cgi-align3.should-get
-!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DIR/data/msa3.fa
+!LAUNCH: export REQUEST_METHOD=POST ; export CONTENT_TYPE=test ; $LAUNCHER $VIDJIL_DIR/browser/cgi/align.cgi < $VIDJIL_DATA/msa3.fa

 $ no spurious info
 0: .* bp in .* sequences

--- a/algo/tests/should-get-tests/chimera-fake-2.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-2.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -t 0 -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake.fa

 $ The KmerSegmenter segments the three chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 3

--- a/algo/tests/should-get-tests/chimera-fake-D.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-D.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-D.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-D.fa

 $ The KmerSegmenter segments the chimera reads on PSEUDO_MAX12 germline (-2)
 f1:unexpected .* -> .* 2

--- a/algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ-germlines-trim.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ-trim.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ-trim.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) .g with special parameters for the algorithm

 $ The KmerSegmenter segments no read in Y because of the parameter

--- a/algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ-germlines.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/data/chimera-fake-VJ.g $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DATA/chimera-fake-VJ.g $VIDJIL_DATA/chimera-fake-VJ.fa
 # Testing a custom (fake) germlines.data

 $ Report the species

--- a/algo/tests/should-get-tests/chimera-fake-VJ.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-VJ.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DIR/data/chimera-fake-VJ.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -g $VIDJIL_DIR/germline -2 $VIDJIL_DATA/chimera-fake-VJ.fa

 $ The KmerSegmenter segments the five chimera reads on PSEUDO_MAX12 germline (-2)
 1:unexpected .* -> .* 5

--- a/algo/tests/should-get-tests/chimera-fake-half.should-get
+++ b/algo/tests/should-get-tests/chimera-fake-half.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DIR/data/chimera-fake-half.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -e 100 -A -t 0 -g $VIDJIL_DIR/germline -4 $VIDJIL_DATA/chimera-fake-half.fa
 # TODO: a more precise modeling should give a e-value computation that could make this work even with -e 1

 $ The KmerSegmenter segments the six chimera reads on PSEUDO_MAX1U germline (-4)

--- a/algo/tests/should-get-tests/chimera-fake.should-get
+++ b/algo/tests/should-get-tests/chimera-fake.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-fake.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-fake.fa

 $ Do not segment on any germline, even incomplete
 1:junction detected in 0 reads

--- a/algo/tests/should-get-tests/chimera.should-get
+++ b/algo/tests/should-get-tests/chimera.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DIR/data/chimera-trg.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -A -uU -g $VIDJIL_DIR/germline $VIDJIL_DATA/chimera-trg.fa

 $ Do not segment on IGL by chance
 f1:IGL .* -> .* 0

--- a/algo/tests/should-get-tests/clones_lec.should-get
+++ b/algo/tests/should-get-tests/clones_lec.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DIR/data/segment_lec.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -c clones -A -3 $VIDJIL_DATA/segment_lec.fa

 $ Extract 50bp windows (TRG)
 1:found . 50-windows

--- a/algo/tests/should-get-tests/clones_simul.should-get
+++ b/algo/tests/should-get-tests/clones_simul.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DIR/data/clones_simul.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 1 -r 1 $VIDJIL_DATA/clones_simul.fa

 $ Junction extractions
 1:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/clones_simul_cluster.should-get
+++ b/algo/tests/should-get-tests/clones_simul_cluster.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DIR/data/clones_simul.fa ; cat out/clones_simul.vidjil
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -k 14 -w 50 -c clones -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -y 3 -z 0 -r 1 -n 5 $VIDJIL_DATA/clones_simul.fa ; cat out/clones_simul.vidjil

 $ Window extractions
 2:found 25 50-windows in 66 reads

--- a/algo/tests/should-get-tests/common-V-D.should-get
+++ b/algo/tests/should-get-tests/common-V-D.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DIR/data/common-V-D.fa  ; cat out/common-V-D.affects
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -KA -z 0 -s \\\\#\\\\#\\\\#\\\\#\\\\#-\\\\#\\\\#\\\\#\\\\#\\\\# -V $VIDJIL_DIR/germline/homo-sapiens/IGHV.fa -J $VIDJIL_DIR/germline/homo-sapiens/IGHJ.fa -D $VIDJIL_DIR/germline/homo-sapiens/IGHD.fa   $VIDJIL_DATA/common-V-D.fa  ; cat out/common-V-D.affects

 $ Segments the sequence
 1: SEG  .* -> .* 1 

--- a/algo/tests/should-get-tests/example_mouse.should-get
+++ b/algo/tests/should-get-tests/example_mouse.should-get
-!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DIR/data/example_mouse.fa
+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -3 -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DATA/example_mouse.fa

 $ Segment sequence on IGK
 1:segIGK.*IGKV.*IGKJ